DNA microarrays used as gene chips are high-throughput devices used to determine the expression profiles of many genes simultaneously. DNA microarrays are used in the fields of molecular biology and medicine for basic research, disease diagnostics and drug discovery. The basis of microarray detection is the ability of a given nucleic acid target molecule to bind specifically to, or hybridize with, a nuclear acid probe having a complementary nucleic acid via Watson/Crick base pairing. In microarrays, nucleic acid probes, each being complementary to a particular target nucleic acid encoding particular information, are immobilized in an arrayed manner to a specific designated position on a substrate. The presence of a target nucleic acid in a sample will result in the hybridization of the target nucleic acid with the immobilized nucleic acid probe, which has a complementary nucleic acid sequence to the target nucleic acid. As the specificity of nucleic acid hybridization is highly dependent on the level of complementary bases between the probes and target nucleic acids, detection of a specific target nucleic acid requires the immobilization of the specific probe, which is optimal for the capture of the target nucleic acids. Hybridization conditions such as buffer, temperature and incubation time can also affect the specificity of the hybridization. Hence, depending on stringency of the hybridizing conditions, probes can bind to target nucleic acids that are less than 100% complementary. Thus to ensure optimal hybridization, hybridization conditions need to be tailored to individual sets of DNA probes.
In known microarray detection systems, the detection of a successful hybridization is usually undertaken optically by the detection of fluorescence from the sample nucleic acids, which have been pre-labeled with a fluorophore bound to the immobilized nucleic acid probe. However, a rather complex laser optical detection system is required for detection of the fluorescence, which is a major drawback.
DNA microarray chips are generally considered as a single use product. However, some DNA microarray chips have been be re-used although their stability does decrease with reuse. To reuse a microarray, the arrays can be treated with heat or base-pH treatment to denature the duplex between the probe and target nucleic acid. The stripped array can then be reused for another re-hybridization with sample nucleic acids. Unfortunately, depending on the type of surface attachment used to immobilize the probe, the signal generally reduces by about 30%-50% after three or more rounds of stripping and re-hybridization.
Once the probes have been spotted to the array chip, the information that can be derived from the chip is limited only to the information that the immobilized probes are meant to capture. For example, DNA arrays used for detection of insulin expression cannot be used for detection of actin expression. This limited reusability of the DNA microarray chip, inflexibility of probe spotted array chips and expensive detection equipment gives rise to high costs for using microarrays, especially in the diagnostic sector where a large number of samples need to be tested.
With the development of microelectronic technology, the use of semiconductor technology in DNA microarrays has been utilized. Instead of measuring fluoresence intensity, changes in electrical current may be used to detect or “readout” successful hybridization. Use of semi-conductor technology for DNA microarrays requires the immobilization of the nucleic acid probe to the silicon surface of a field effect transistor (FET). Hybridization of target nucleic acid with a nucleic acid probe elicits a change in resistance, and in turn the current flowing through the FET, which constitutes the basis of the readout of the microarray assay. However, because of the relatively weak donating and withdrawing effects of small charged nucleic acids, a sufficient amount of hybridization between sample nucleic acids and probes is required to induce a measurable resistance change. The use of silicon nanowire (SiNW) as the surface for nucleic acid immobilization helps negate this former problem.
SiNW are silicon wires with diameters constrained to tens of nanometers or less and which exhibit unique properties such as super conductance. SiNW are ultra-sensitive FET biosensors that allow a small localization of charge to become a significant gate to the flow of current in the FET.
DNA has been used in nucleic acid probes for capture of target nucleic acids in microarrays. However, DNA, being negatively charged, does suffer from drawbacks when used in nucleic acid probes for SiNW arrays. This is because the natural negative charges of the DNA probes results in the formation of a densely charged layer at the surface of the silicon substrate which in turn induces a strong electrical field at the SiNW surface. This in turn increases the background noise of the baseline signal generated by the SiNW. Therefore, to induce significant charge variation in the SiNW FET, a significant amount of target nucleic acids are required to be bound to the DNA probes in order to overcome the high noise baseline. This makes the detection of small amounts of target nucleic acids difficult. DNA, being a natural polymer, is also easily degraded by enzymes found in the samples or the environment. This in turn reduces the reusability of the SiNW biosensor.
Therefore, there is a need to provide a sensor, which overcomes, or at least ameliorates, one or more of the disadvantages described above.